Labs
Lab writeups:
Week 2 Lab: Restriction Digests
Protocol Part 0: Design Note: Ignore EcoRI lane: for visualization Note: We are using DNA from mycobacteriophage Kampy Part 1a: Gel prep Setting up a 1% agarose gel:
Design Python Code from opentrons import types metadata = { # see https://docs.opentrons.com/v2/tutorial.html#tutorial-metadata 'author': '', 'protocolName': '', 'description': '', 'source': 'HTGAA 2026 Opentrons Lab', 'apiLevel': '2.20' } ############################################################################## ### Robot deck setup constants - don't change these ############################################################################## TIP_RACK_DECK_SLOT = 9 COLORS_DECK_SLOT = 6 AGAR_DECK_SLOT = 5 PIPETTE_STARTING_TIP_WELL = 'A1' well_colors = { 'A1' : 'Red', 'B1' : 'Green', 'C1' : 'Orange' } def run(protocol): ############################################################################## ### Load labware, modules and pipettes ############################################################################## # Tips tips_20ul = protocol.load_labware('opentrons_96_tiprack_20ul', TIP_RACK_DECK_SLOT, 'Opentrons 20uL Tips') # Pipettes pipette_20ul = protocol.load_instrument("p20_single_gen2", "right", [tips_20ul]) # Modules temperature_module = protocol.load_module('temperature module gen2', COLORS_DECK_SLOT) # Temperature Module Plate temperature_plate = temperature_module.load_labware('opentrons_96_aluminumblock_generic_pcr_strip_200ul', 'Cold Plate') # Choose where to take the colors from color_plate = temperature_plate # Agar Plate agar_plate = protocol.load_labware('htgaa_agar_plate', AGAR_DECK_SLOT, 'Agar Plate') ## TA MUST CALIBRATE EACH PLATE! # Get the top-center of the plate, make sure the plate was calibrated before running this center_location = agar_plate['A1'].top() pipette_20ul.starting_tip = tips_20ul.well(PIPETTE_STARTING_TIP_WELL) ############################################################################## ### Patterning ############################################################################## ### ### Helper functions for this lab ### # pass this e.g. 'Red' and get back a Location which can be passed to aspirate() def location_of_color(color_string): for well,color in well_colors.items(): if color.lower() == color_string.lower(): return color_plate[well] raise ValueError(f"No well found with color {color_string}") # For this lab, instead of calling pipette.dispense(1, loc) use this: dispense_and_detach(pipette, 1, loc) def dispense_and_detach(pipette, volume, location): """ Move laterally 5mm above the plate (to avoid smearing a drop); then drop down to the plate, dispense, move back up 5mm to detach drop, and stay high to be ready for next lateral move. 5mm because a 4uL drop is 2mm diameter; and a 2deg tilt in the agar pour is >3mm difference across a plate. """ assert(isinstance(volume, (int, float))) above_location = location.move(types.Point(z=location.point.z + 5)) # 5mm above pipette.move_to(above_location) # Go to 5mm above the dispensing location pipette.dispense(volume, location) # Go straight downwards and dispense pipette.move_to(above_location) # Go straight up to detach drop and stay high ### ### YOUR CODE HERE to create your design ### pipette_20ul.pick_up_tip() pipette_20ul.aspirate(17, location_of_color('Red')) cursor = center_location.move(types.Point(x=-17.6, y=28.6)) # draw stars for i in range(3): dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x, y=cursor.point.y-2.2)) dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x-4.4, y=cursor.point.y-2.2)) for j in range(5): dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x+2.2, y=cursor.point.y)) cursor = center_location.move(types.Point(x=cursor.point.x-8.8, y=cursor.point.y-2.2)) for j in range(3): dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x+2.2, y=cursor.point.y)) cursor = center_location.move(types.Point(x=cursor.point.x-8.8, y=cursor.point.y-2.2)) for j in range(5): dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x+2.2, y=cursor.point.y)) cursor = center_location.move(types.Point(x=cursor.point.x-6.6, y=cursor.point.y-2.2)) dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x, y=cursor.point.y-2.2)) dispense_and_detach(pipette_20ul, 1, cursor) if i < 2: pipette_20ul.aspirate(17, location_of_color('Red')) cursor = center_location.move(types.Point(x=cursor.point.x+17.6, y=cursor.point.y+13.2)) # draw stripes pipette_20ul.aspirate(15, location_of_color('Red')) cursor = center_location.move(types.Point(x=cursor.point.x-50.6, y=cursor.point.y-6.6)) # two stripes for i in range(2): # six rows per stripe for j in range(6): # two refills per row for k in range(2): # fifteen dots per refill for l in range(15): dispense_and_detach(pipette_20ul, 1, cursor) cursor = center_location.move(types.Point(x=cursor.point.x+2.2, y=cursor.point.y)) pipette_20ul.aspirate(15, location_of_color('Red')) if j < 5: cursor = center_location.move(types.Point(x=-33, y=cursor.point.y-2.2)) if i < 1: cursor = center_location.move(types.Point(x=-33, y=cursor.point.y-6.6)) # Don't forget to end with a drop_tip() pipette_20ul.drop_tip()
See Week 4 Homework tab for lab work.
See Week 4 Homework tab for lab work.
PCR Setup Purple and Orange NFW – added fwd - Pu, added fwd - O, added rev – same for both, added Master mix – added Template plasmid – added Calculated PCR params and started running Need to add DPN1 to digest the template DNA from the PCRs for w/out template DPN1 currently at -20 BEL – thaw for a bit 1 ul DPN1 to ea rxn (put back into freezer)